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When President Bush signed a secret executive order in July barring “cruel, inhumane and degrading treatment” of high value “detainees” in the War on Terror, there was no addendum laying out which of the detainees had faced harsh treatment in the past, nor was there a detailing of what the treatment entailed.

However, an NBC News investigation has learned that a total of 13 high value detainees— all of them ranking al-Qaida operatives—were subjected to “enhanced interrogation techniques” in 2002 through 2004. The techniques in some cases have been abandoned because they have become controversial; while others are still being practiced by interrogators.

In interviews, current and former high-ranking U.S. intelligence officials, tell NBC News that the most controversial of the “enhanced interrogation techniques,” including water-boarding, were used on only three detainees—Abu Zubaydah, who directed al Qaeda’s terrorist training camps; Khalid Sheikh Mohammed, the mastermind of the 9-11 attacks; and Hambali, the mastermind of the Bali bombings in 2002. In water-boarding, a detainee’s head is covered with a fabric or cellophane and a steady flow of water is poured into his nostrils, creating the sensation of drowning. It is meant to make the detainee believe he was being slowly and methodically executed.

The enhanced interrogation measures include sleep deprivation, exposure to extreme heat and cold, confined quarters, and psychological and physical abuse along with the use of psychotropic drugs, say officials.

Intelligence officials tell NBC News then CIA Director George J. Tenet ordered a suspension of the enhanced measures in early 2004, as torture allegations mounted. The Abu Ghraib prison revelations, beginning in April 2004, was a major factor in the decision to suspend the measures, said intelligence officials. But the main concerns, they added, were legal: Could CIA officials, including both the interrogators and their superiors, ultimately be prosecuted?President Bush’s order in July removed a lot of those legal concerns, as CIA Director Gen Michael V. Hayden stated in an e-mail to agency employees hours after the order was issued.

“The President’s action— along with the Military Commissions Act of 2006— gives us the legal clarity we have sought. It gives our officers the assurance that they may conduct their essential work in keeping with the laws of the United States,” wrote Hayden.

In a speech and question and answer session at the Council on Foreign Relations last week, Hayden declined to provide detail on the interrogations. He would neither discuss the specific techniques, saying only that the new rules help the CIA “exhaust the universe of interrogation techniques allowed under common article three” of the Geneva Conventions. Hayden did say that fewer than 100 suspected terrorists had been detained by the agency.

“Since [the CIA’s detention and interrogation program] began with the capture of Abu Zubaydah in 2002, fewer than one hundred people have been detained at CIA’s facilities. And the number of renditions, apart from the fewer than one hundred detainees, is an even smaller number,” said Hayden, referring to the practice of sending detainees back to their home countries.

Hayden added that 70 percent of the information contained in the National Intelligence Estimate on the terrorist threat, which was released in July, came from the interrogation of detainees.

Detainees interrogated with enhanced measures
The 13 who were subjected to the enhanced measures, according to the investigation, included all but two of the 15 high value detainees recently transferred to Guantanamo Bay, Cuba and set for trial as enemy combatants. The two who were not subjected, said one official, were the last two detainees captured, Abu Faraj al Libi and Abu Hadi al Iraqi. Abu Faraj, the group’s No. 3 as director of external operations, was captured in May 2005 while al-Iraqi, liaison between al Qaeda and al Qaeda in Iraq, was captured in December 2006. Both were grabbed after the suspension order.

Among those subjected to the enhanced techniques are operatives responsible for the attacks on the East Africa embassies in 1998, the USS Cole in 2000, and the September 11 attacks. The interrogations took place at secret U.S. prisons in eastern Europe and north Africa.

The three subjected to water boarding were viewed as al-Qaida operatives with “real-time information” on terrorist planning:

Khalid Sheik Mohammed, mastermind of 9-11; and the man who killed Daniel Pearl; and

Hambali, the Indonesian terrorist responsible for the Bali bombings in December 2002 that killed more than 200, including five Americans.

Two of the three—KSM and Hambali—were chosen for water boarding because they were resistant to other interrogation methods…one, Zubaydah, because he initially told the CIA of an impending attack, then refused to discuss it, according to two officials.

A fourth high ranking al-Qaida member, Ramzi bin al Shibh—organizer of the Hamburg cell that was the core of the 9-11 attacks—agreed to talk with just the threat of water-boarding, said the officials.

Decision-making and monitoring
Although the CIA will not comment on the subject, former CIA Director Tenet wrote about the rationale and the decision-making that went into the choice of those subjected to the most “aggressive measures”… as well as safeguards.

In his book, “At the Center of the Storm”, Tenet wrote:

“The administration and Department of Justice were fully briefed on these tactics. After we received the written Department of Justice guidance on the interrogation issue, we briefed the chairmen and ranking members of our oversight committees. While they were not asked to formally approve the program as it was done under the President’s unilateral authorities, I can recall no objections being raised.

“The most aggressive interrogation methods were applied to only a handful of the worst terrorists on the planet, including people who had planned the 9-11 attacks and who among other things were responsible for Daniel Pearl’s death”… an obvious reference to KSM.

The interrogations, he adds, “were precisely monitored” and were aimed at preventing “follow on attacks”. He claims, as has the White House, that the interrogations did prevent attacks in “the U.S., United Kingdom, Middle East, Southeast Asia and Central Asia”.

One former official said at least four agency personnel observed each of the interrogations, two of them medical personnel.

'Cried like a baby,' playing on weaknesses
According to multiple officials, the detainees reacted differently to the most extreme measures. Hambali, for example, quickly told all he knew — “cried like a baby” after his first water boarding session, recounted another official. KSM underwent at least two sessions and other extreme measures before talking. "KSM required, shall we say, re-dipping," said another former senior intelligence official.

Bin al Shibh was viewed as a weakling and a narcissist and the agency played heavily on that. He quickly became the most cooperative of those detained, although he recent months he has once again refused to talk.

And although the detainees were segregated and guarded 24 hours a day, officials say they were clever enough to find ways of communicating.

Not everyone in the agency thought the use of water-boarding and other such techniques was productive. Some of those interrogated quickly provided threat information to “stop the pain,” as one put it. That stopped the interrogation sessions while the agency and law enforcement tracked down the tip, some of which turned out to be disinformation.

New executive order
But in conference call last week, a senior administration official refused to discuss which techniques might be used under the new executive order.

“I’m not in a position to talk about any specific interrogation practices,” said the official when asked about water boarding. “And I think the President has made it clear from the beginning of the debate here that it’s really impossible for us, consistent with the objectives of such a program, to publicize to the enemy what practices may be on the table, what practices may be off the table, and that that will only allow al-Qaida to train against those that they know are on or off.”

(Officials have previously said that the detainees were able to figure out clever ways of communicating, even while in the secret prisons.)

The official did note that sleep is not a “basic necessity of life” as laid out in the Geneva Conventions. He did suggest that using extreme heat and cold would not be available to agency interrogators in the future, under the executive order.

“It requires that all detainees in the program receive the basic necessities of life, including adequate food and water, shelter from the elements, necessary clothing, protection from extremes of heat and cold and essential medical care.”